[English] 日本語
Yorodumi
- PDB-7jgu: Structure of FN3tt mut -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jgu
TitleStructure of FN3tt mut
ComponentsFibronectin type-III domain-containing protein
KeywordsSTRUCTURAL PROTEIN / FN3-like domain / Hyperthermal stability / Surface Salt Bridges
Function / homology
Function and homology information


IPT/TIG domain / ig-like, plexins, transcription factors / IPT domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Fibronectin type-III domain-containing protein
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLuo, J. / Boucher, L.E.
CitationJournal: Proteins / Year: 2022
Title: Surface salt bridges contribute to the extreme thermal stability of an FN3-like domain from a thermophilic bacterium.
Authors: Boucher, L. / Somani, S. / Negron, C. / Ma, W. / Jacobs, S. / Chan, W. / Malia, T. / Obmolova, G. / Teplyakov, A. / Gilliland, G.L. / Luo, J.
History
DepositionJul 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fibronectin type-III domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4142
Polymers11,1751
Non-polymers2381
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.000, 38.310, 28.180
Angle α, β, γ (deg.)90.000, 103.880, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-227-

HOH

-
Components

#1: Protein Fibronectin type-III domain-containing protein


Mass: 11175.329 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) (bacteria)
Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: TTE0165 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RD81
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5 / Details: 25% PEG 3350, 0.2M sodium di-hydrogen phosphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→27.36 Å / Num. obs: 34160 / % possible obs: 99 % / Redundancy: 3.184 % / Biso Wilson estimate: 19.682 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.06 / Χ2: 0.93 / Net I/σ(I): 12.39 / Num. measured all: 108762 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.2-1.232.9210.9232.557379254325260.5431.12899.3
1.23-1.263.0440.7283.017404246624320.6840.88298.6
1.26-1.33.0890.5263.887328239323720.7780.63999.1
1.3-1.343.2110.4164.677521236023420.8580.50299.2
1.34-1.393.2420.3355.877206223922230.8710.40399.3
1.39-1.433.2270.28177090220321970.8970.33899.7
1.43-1.493.1640.2258.026715213421220.9370.27199.4
1.49-1.553.1930.15910.16396200520030.9670.19199.9
1.55-1.623.4310.1212.326649194619380.9790.14299.6
1.62-1.73.4230.09414.416456189418860.9860.11299.6
1.7-1.793.3190.07116.765832176617570.9920.08599.5
1.79-1.93.1960.0619.055426172516980.9930.07198.4
1.9-2.033.0550.0520.874683156515330.9940.06198
2.03-2.193.0520.04522.494453148514590.9960.05498.2
2.19-2.43.3430.04224.684466135113360.9960.0598.9
2.4-2.683.3010.03925.484054124712280.9960.04798.5
2.68-3.13.1660.03725.753394108310720.9970.04499
3.1-3.792.990.03525.9227519549200.9960.04396.4
3.79-5.373.1780.03727.1822637237120.9960.04498.5
5.37-27.363.2080.03527.1812964194040.9960.04296.4

-
Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JGT

7jgt


Resolution: 1.2→27.36 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1809 1707 5 %
Rwork0.149 32451 -
obs0.1505 34158 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.71 Å2 / Biso mean: 24.7027 Å2 / Biso min: 8.07 Å2
Refinement stepCycle: final / Resolution: 1.2→27.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms706 0 38 97 841
Biso mean--66.17 36.18 -
Num. residues----90
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.240.32641420.2962697283999
1.24-1.280.3041400.28572673281399
1.28-1.320.30931420.25982695283799
1.32-1.370.25451410.19842680282199
1.37-1.440.1981420.146926982840100
1.44-1.510.15741420.129626982840100
1.51-1.610.1541440.124527322876100
1.61-1.730.14581420.11926972839100
1.73-1.90.14261430.12062726286999
1.9-2.180.14741420.12462684282698
2.18-2.750.17151420.15022710285299
2.75-27.360.19011450.14952761290698

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more